Nucleic acid ladders

Abstract

The present invention provides nucleic acid molecules which may be used as standards for estimating the size (in base pairs) and mass of linear, double-stranded or single-stranded nucleic acid molecules separated by size. The nucleic acid molecules of the invention may be DNA molecules, RNA molecules or DNA/RNA hybrid molecules, and may be double-stranded or single-stranded. The invention also provides methods for producing nucleic acid sizing ladders from these nucleic acid molecules, ladders produced by such methods, and methods for estimating the size and mass of nucleic acid molecules by comparison to these nucleic acid sizing ladders.

1 . An isolated nucleic acid molecule comprising two or more repeat-containing sequences having the formula
   (X 1 X 2 ) n        (Y 1 Y 2 ) n      wherein:   X 1  and X 2  are single nucleotides or derivatives thereof which may or may not be identical; Y 1  and Y 2  are single nucleotides or derivatives thereof complementary to X 1  and X 2 , respectively;   and n is an integer from 1 to 1×10 10 ,   and wherein two or more of said repeat-containing sequence copies are separated by a restriction site and the nucleotide compositions of (X 1 X 2 ) n  and (Y 1 Y 2 ) n  are substantially identical.   
     
     
         2 . An isolated nucleic acid molecule of  claim 1  wherein X 1  and X 2  are single nucleotides. 
     
     
         3 . An isolated nucleic acid molecule of  claim 1  wherein Y 1  and Y 2  are single nucleotides. 
     
     
         4 . An isolated nucleic acid molecule of  claim 1  wherein X 1  and X 2  are single nucleotides and wherein Y 1  and Y 2  are single nucleotides. 
     
     
         5 . The nucleic acid molecule of  claim 1 , wherein said nucleic acid molecule is a DNA molecule. 
     
     
         6 . The nucleic acid molecule of  claim 1 , wherein said nucleic acid molecule is an RNA molecule. 
     
     
         7 . The nucleic acid molecule of  claim 1 , wherein said nucleic acid molecule is a DNA-RNA hybrid molecule. 
     
     
         8 . A sizing ladder comprising two or more nucleic acid fragments, wherein said sizing ladder is produced by at least partially digesting the nucleic acid molecule of  claim 1  with a restriction endonuclease that cleaves at said restriction site. 
     
     
         9 . The sizing ladder of  claim 8 , wherein said two or more nucleic acid fragments are of varying sizes, and wherein the size of each nucleic acid fragment is a multiple of the size of said repeat-containing sequence. 
     
     
         10 . The sizing ladder of  claim 8 , wherein said nucleic acid fragments are detectably labeled. 
     
     
         11 . The sizing ladder of  claim 10 , wherein said nucleic acid fragments are detectable labeled with a radiolabel, a fluorescent label or a chemiluminescent label. 
     
     
         12 . A kit comprising one or more containers, wherein a first container contains the sizing ladder of  claim 8 .